[gmx-users] compile template.c

[Mark Abraham]

On 12/08/2011 7:48 AM, Park, Jae Hyun nmn wrote:
> Dear GMX users,
>
> Now, I am trying to write my own gromacs analysis code with gromacs 4.5.3.
> As a first test, when I run "make" in the directory of "template" I got the following message:
>
> ------------------------------
> cc  -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -pthread -I./include  -I/usr/include/libxml2 -I/home/h1y/gromacs-4.5.3s/include    -I/home/h1y/fftw3s/include  -c -o work.o work.c
>
> cc  -L/home/h1y/gromacs-4.5.3s/lib -L/home/h1y/fftw3s/lib   -o work work.o -lmd -lgmx -lfftw3f -lxml2  -lnsl -lm
>
> /home/h1y/gromacs-4.5.3s/lib/libgmx.a(vmddlopen.o)(.text+0x6): In function `vmddlopen':
>
> : undefined reference to `dlopen'
>
> /home/h1y/gromacs-4.5.3s/lib/libgmx.a(vmddlopen.o)(.text+0x11): In function `vmddlerror':
>
> : undefined reference to `dlerror'
>
> /home/h1y/gromacs-4.5.3s/lib/libgmx.a(vmddlopen.o)(.text+0x21): In function `vmddlsym':
>
> : undefined reference to `dlsym'
>
> /home/h1y/gromacs-4.5.3s/lib/libgmx.a(vmddlopen.o)(.text+0x31): In function `vmddlclose':
>
> : undefined reference to `dlclose'
>
> collect2: ld returned 1 exit status
>
> make: *** [work] Error 1
>
>
> I would deeply appreciate if any help why I got those erros and how to figure out.

Probably when the feature of using the VMD libraries was added, nobody 
updated share/template/Makefile.am. You can either disable the use of 
the DLOPEN facility from the VMD libraries (used for reading 
non-GROMACS-native file formats) when you configure GROMACS, or you can 
update share/template/Makefile.am so that

XLIBS = -lmd at LIBSUFFIX@ -lgmx at LIBSUFFIX@ @FFT_LIBS@ @XML_LIBS@ 
@GSL_LIBS@ @LIBS@

becomes

XLIBS = -lmd at LIBSUFFIX@ -lgmx at LIBSUFFIX@ @FFT_LIBS@ @XML_LIBS@ 
@GSL_LIBS@ @LIBS@ @DLOPEN_LIBS@

Then get the bootstrap script from a git install of GROMACS and run that 
from the main source directory, before configure, make, make install. 
Now the installed template Makefile should be able to link properly.

Mark